To investigate simultaneous Cr(VI) reduction and Zn(II) biosorption by a microorganism. A new isolate, Stenotrophomonas sp. TD3, simultaneously reduced Cr(VI) and achieved Zn(II) biosorption. The strain was resistant to other metals and salts, and its Zn biosorption could be stimulated greatly by CaCl2 and MgCl2, which has not been reported previously. Three putative Cr- or Zn-related genes, chrR, zupT and hmrE, were amplified and measured using quantitative real-time PCR to evaluate their mRNA expression levels in Stenotrophomonas sp. The three putative genes were not sensitive to Cr6+, Zn2+, Ca2+, and Mg2+, which suggested that they were constitutively expressed in Stenotrophomonas sp. TD3. These results improve our understanding of the mechanism and suggest that the strain is a potential candidate for facilitating remediation of Cr(VI) and Zn contaminated sites.